In business school the first thing they teach you about CEOs is: it is the CEO’s job to increase the shareholder value of the company. Since taking the position Ballmer has decreased shareholder value, as reflected by stock price, by -56.63%. That. Is. Not. Good . . . Microsoft should be searching for a new CEO right now.

I suppose one cannot argue with the fact that Windows is the best general purpose OS out there. Other OSes may prove to be better in the more expert related scenarios.
I think Windows has the broadest spectrum of tasks which can be performed "pretty well".

For "general purpose OS" let's say a kernel that can be used across a broad spectrum of the computing marketplace - fuzzy, but I think close enough.

For "Windows" we'll use the NT kernel, and for "Linux" the Linux kernel.

Now, let's compare Windows to Linux on those terms.

For market entry cost, Linux has the advantage of skipping the legal negotiating with Microsoft for a custom license, no one-time or per unit royalty payments, and for having the complete source code available for modification and rebuild optimized for a new market thus avoiding shims and work-arounds. Windows has Microsoft's famed developer support organization behind it (for a price), but using them under non-disclosure runs the risk of Microsoft stealing your market out from under you as they have so famously in the past. If your product is based largely on providing a general purpose desktop computer running a specific package available only on Windows, of course, Windows is a no-brainer - but that market is thoroughly saturated, and with such a low barrier to entry you would run a high risk of being overrun by a larger competitor able to negotiate a sweetheart deal with Microsoft. For entry cost to most viable markets, then, I would argue that Linux gets you there cheaper and more safely, and is thus "best". Note the number of innovative products launching with Linux today as corroborating evidence.

For greatest potential for differentiation, it's not even close. Linux permits you to do anything with the code, while Windows comes with a long list of constraints to be negotiated. Linux does require those who distribute modified kernels to make the source available; if we were considering BSD, it would probably be "best" of three by this criteria, but Linux is clearly "better" than Windows in this context. Again, you'll probably notice much more differentiation with Linux and BSD products than Windows products - tablets would be a golden case study, for example.

For most scalable, it is again not even close. Linux powers a plurality of the smartphones in the world, over 90% of the supercomputers in the world, and everything in-between. It scales to a USB-size complete computer, watches, even pellets in paint. It's scalability is legendary. For practical use, Windows scales only from netbooks and tablets to enterprise servers. (Windows Phone 7 has a different kernel, of course, though much of the development infrastructure is shared.) In scalability, Linux has proven itself "best" by a clear margin.

It's in market penetration that you probably consider Windows "best", but here it's more tricky. Windows was ruled a desktop monopoly in the 1998, and that hasn't changed much - together, OS/X and Linux and "others" hold less that 10% installed base and at most 15% of each quarter's market (sales) share. In servers, Windows has the best revenue stream, but holds installed base roughly equivalent to Linux. But in virtually every other market segment of significance, Linux has "better" market penetration than Windows. Perhaps this is why Microsoft's market cap has famously halved during Mr. Ballmer's tenure - Microsoft's revenue stream is still desktop / server Windows, Office, and debris.

My suspicion is that your remarkably broad claim really meant "Windows has more desktop applications than any other OS" or "commercial Windows desktop applications have more income potential than any other OS". I would agree with both of those statements. Deep down, I suspect you meant "It's best for me", and I couldn't argue with that, either, though it's not a very useful assertion for everyone else. I would also agree that "Microsoft provides world-class support for desktop and server application developers" - it may or may not be "best", but it's excellent.

But Windows isn't "best" by most other definitions of "best", and it's far less general purpose than many of its competitors, as a broad look at the market will attest.

I'm sorry, it appears I was misunderstood. Best general purpose from the end-user perspective, that's what I meant.
A user can browse the web, use office stuff, playing games - all in an overall good experience on the same OS.

As for some of your other points, once you have the source code it's obvious that you can do whatever you want with it.
But I think that's a poor solution. A system should be built extensible, and from my personal experience, having used both platforms for quite some time, windows is more extensible. Just so that we're clear, I'm referring to it at the desktop level. The kernels both have extensibility points.